The House of Life

I’ve had one of my mathematical days today, and my head is full of sines and cosines. I did what I wanted to do, which was to build a computer simulation model of a 2D cell growing and dividing, in two different ways. I was almost going to go on and produce another variant, but my brain ran out of cosines, and so instead I’ve broken open a bottle of Beck’s, and dropped a couple of slices of lemon in it, and started wondering…

For the past year, since I moved from Devon to Herefordshire, I seem to have become something of a theoretical biologist, first building computer simulation models of cell population growth, and then building computer simulation models of cell growth and division.

I don’t know whether there actually are such things as theoretical biologists. I did a search for it online a while back, and it seems there actually are such creatures out there, and they build computer simulation models too. But generally when I think of biologists, I think of people peering through microscopes at cells, or hunting butterflies in Amazon forests. They’re people who look at living things and classify them and dissect them and photo them.

Biology was one thing I never studied at school. It wasn’t that I wasn’t interested. It was because I really hated the smell that came out of the school biology lab. I think it was the smell of formaldehyde, and it was the most godawful smell in the world. Some people say that tobacco smoke “stinks”, but if tobacco smoke stinks, what the heck does formaldehyde do? Because I thought it was such an awful smell that I couldn’t contemplate ever spending more than 10 seconds in the school biology lab. In fact, I never went inside it once. The overpowering stench of the place stopped me in my tracks yards outside the front door.

I think they used it as a preservative. As far as I could make out, they spent their time dissecting frogs and catfish and stuff. Which I could sort of understand, except that it seemed to me that if you’re studying dead catfish and dead frogs you’re not, well,… you’re not studying living things, are you? You’re studying dead things. I had the same feeling when I wandered round the natural history museum in Kensington, full of dinosaur skeletons, all of them very, very dead. I wanted to understand living things, not dead things.

Not that I have a clue what formaldehyde is, because I didn’t study chemistry either. But I at least got inside a chemistry lab, because they generally didn’t smell quite as bad as biology labs did. Although our one had a fume cupboard in which there was a mountain of glass that produced hydrogen sulphide – which is also pretty malodorous stuff, but not (in my opinion) half as bad as formaldehyde. But although I actually got inside a chemistry lab, I could never understand much chemistry. The chemistry master would write chemical equations up on the board which were like 2H2 + N02 –> H2NO + H2O or something, and I’d wonder why it couldn’t just be 2H2 + N02 –> H4N02. A brand new compound that could dissolve glass. I never did understand, and gradually spiralled down to the bottom of the class. I spent most of my time hiding behind the bottles, hoping I wouldn’t get asked anything. Because if I was, I was almost certain not to know the answer. Eventually I gave up chemistry completely. Which was unusual for me. Most subjects I could do pretty well, but not chemistry.

I didn’t have the same problems with maths and physics. Which may have been because the maths classroom and the physics lab didn’t have their own godawful stygian pong. Say what you like about them, but there’s one good thing about equations: they don’t smell of anything.  You don’t have to wash your hands for half an hour after you’ve solved a few simultaneous equations.

Many years later, I came across a book called Physical Chemistry which explained chemistry in terms of physics. All the mysterious bonds between atoms were explained in a completely new way, and a way I could understand, and I wished that I’d been taught chemistry that way. One day I’ll buy myself a book of Physical Chemistry, and become engrossed in it, because it’ll be like reading a thriller.

So it means that, if I’m a theoretical biologist at all (and I’m probably not even that), I’m a theoretical biologist who knows very little about biology, and even less about chemistry. But that hasn’t deterred me from thinking about living things. I just think about them using things that I do understand, like simple physics and simple mathematics. And I build simple theoretical models of simple living things using simple physics and simple mathematics. They’re models of a kind that nobody else uses, because I’m the only one who uses them. They’re abstract models that I’ve slowly pieced together myself, over many years.

What it means is that I look at living things very differently than most biologists do. I look at it through mathematical-physical eyes, which they never seem to do. They seem to look at it through chemical eyes (the ones I can’t see through, because I’m chemically blind).

When I look at cells, I see things that have got length and breadth and mass and volume and geometry. Lots and lots of geometry. And I see things that gain and lose energy, and which are being pushed and shoved by other cells around them. And which are being stretched and squeezed and twisted and crushed and bent.

And it really puzzles me that biologists don’t see them that way too. But it seems they don’t. I’ve got a book this thick on molecular cell biology that I bought about 20 years ago, when I started getting interested in cells and biology. It’s beautifully illustrated. It’s a work of art. But it’s chock full of chemistry, and there’s next to no physics or mathematics in it.

It seems to me that the biologists have a pretty complete chemical understanding of living things. They know exactly what living things are made of. And they even know how living things make their chemical constituents. They unpackaged the citric acid cycle, and they’ve unwound DNA. They know everything.

But to me that seems like knowing that a house is made of bricks and mortar and timber and glass and tiles, and even knowing exactly how bricks and mortar and timber and glass are manufactured, but not having an understanding of how the whole house works as a piece of architecture, as a whole. And they don’t seem to see it that way at all. It’s as if they’re as blind to mathematics and physics as I am blind to chemistry.

Because for me a cell is the House of Life, and I look at it like an architect would look at it, or maybe a structural engineer (because I was taught those ways of seeing). I look at the geometry of the whole thing. I look at the stresses and strains that are exerted in it. For me, it’s not chemistry: it’s geometry and physics.

And looking at cells in the funny theoretical way that I do, I’ve been looking at cancer. Because cancer is a cellular disorder whereby cancer cells just keep on growing and dividing. And so it was only natural, after I’d come up with a new explanation of how cells divide (which isn’t quite the same as the textbook explanation) that I’d start to wonder how cancer cells grew and divided.

And I’ve maybe begun to understand cancer a bit. I think I can understand the geometry of cancer a little bit. Only fractionally maybe. But enough to feel able to write something about it that might provide an interesting new perspective on it.

And maybe it’ll help. After all, it’s us smokers with our smoking that’s supposed to be the root cause of all cancer. It might help for one of us to come up with another idea. After all, in 60 years, they don’t seem to have made any progress, beyond banning smoking almost everywhere.

So maybe later on this week, I’ll try to write something about cancer. I’ll try and steer clear of mathematics, and make it as easy to understand as possible. I’ll try to keep it simple and graphical. And I hope that, if nothing else, it’ll make cancer seem a bit less terrifying, and a lot more interesting. Because that’s how it’s become for me.

About Frank Davis

smoker
This entry was posted in Uncategorized. Bookmark the permalink.

23 Responses to The House of Life

  1. waltc says:

    Trouble trying to enter data. Filled out one form, hit submit. Which led to a cockeyed frame in mouse type that required extreme left/ right scrolling to not-quite-decipher but which began with something like “there was an error in your SQL” (?) whatever the hell that is, and which seemed to have encrypted, but also scrambled, the answers I’d entered. A new form appeared below this strange soup but everything on it was out of alignment and screwed up. I also have no idea if the first form actually submitted at all.

    Dunno if part of the problem is my c. 2006 computer (I just ordered a new one to arrive in 2 wks) or with the system itself. But something’s not working. Worse comes to worst, just give me a brick address and I’ll mail them.

  2. Frank Davis says:

    I’ve not had this problem. I’ll refer it to Wiel.

    But if necessary, I’ll give you a brick address. We’ll get the data somehow.

    • Walt says:

      I could work out a way to just email the stuff in some organized grid and include a pdf doc attachment. Ultimately more trouble than snailing, but no less trouble than filling out the forms. In fact, perhaps simpler. BTW, you want us to hold on to the hard copies against the day Glantz demands raw data (of the kind he himself never turns over)?

      • Frank Davis says:

        BTW, you want us to hold on to the hard copies against the day Glantz demands raw data (of the kind he himself never turns over)?

        Yes, please. Keep in some safe place. Unless of course you mail them to me.

      • Wiel Maessen says:

        I need it in the database to be able to do stats on it. If it’s sent in in pdf format, I would need to enter all forms by hand myself.
        Can you send me the error message so I can fix the error? I guess you just forgot to fill in one field that I didn’t expect to come in empty.

  3. Woodsy42 says:

    “You don’t have to wash your hands for half an hour after you’ve solved a few simultaneous equations.”
    No- you have to wash your brain out with a good malt or immerse you intellectual capacity in brain numbing TV soaps or something, (or sex is good).
    But more seriously Frank. Something that struck me recently . Most of the modern ideas and inventions – electricity, machines, radio, cars etc that we use every day were not invented by specialised scientists. They were invented by educated ‘all-rounders’, Of course they were often people with time and huge wealth who could indulge their interests, but nevertheless they were amateurs with a rounded knowledge who put known ideas together into something different.

    • Frank Davis says:

      It’s an interesting subject. I guess the way that I see it is that if you’ve been taught about something – like biology – you’ve been handed a whole way of looking at it, a shared understanding. You become one of the gang, and your qualifications reflect your standing within it. And maybe what you know is all good stuff too. But it makes it hard for you to think ‘outside the box’, because your education has put you in an invisible box, and framed and shaped all your thinking.

      The other thing is that, as a specialised scientist, you’re usually constrained (paid) to think about a pretty narrow field. If you’re going to find out anything new, it’s going to be something of a pretty restricted sort.

      I’m not at all wealthy, but I have acres of idle time at my disposal, and thinking and writing and playing around with equations isn’t expensive. Nor, these days, are computers very expensive either. And we also have the wonderful library of the internet at our disposal.

      • Junican says:

        Not to forget that they can all talk to each other in language that they all speak and understand. That makes it very difficult to use imagination since there are no words to describe new things. As an example, I can mention Michael Faraday. When he gave lectures on electricity and magnetism at the Royal Society, he used language which his audience could understand. It appears that he did not much like the calculus language which Maxwell spoke in.

  4. Rose says:

    And I hope that, if nothing else, it’ll make cancer seem a bit less terrifying, and a lot more interesting

    I found this very interesting when I found it.

    “A new interest in the relationship between niacin and cancer has evolved from the discovery that the principal form of this vitamin, NAD, is consumed as a substrate in ADP-ribose transfer reactions.

    Poly(ADP-ribose) polymerase, an enzyme activated by DNA strand breaks, is the ADP-ribosyltransferase of greatest interest with regard to effects on the niacin status of cells since its Km for NAD is high, and its activity can deplete NAD.”

    http://www.jacn.org/content/12/4/412.abstract

    niacin formerly known as nicotinic acid.

    “Poly (ADP-ribose) polymerase (PARP) is a family of proteins involved in a number of cellular processes involving mainly DNA repair and programmed cell death.

    PARP is found in the cell’s nucleus. The main role is to detect and signal single-strand DNA breaks (SSB) to the enzymatic machinery involved in the SSB repair. PARP activation is an immediate cellular response to metabolic, chemical, or radiation-induced DNA SSB damage. Once PARP detects a SSB, it binds to the DNA, and, after a structural change, begins the synthesis of a poly (ADP-ribose) chain (PAR) as a signal for the other DNA-repairing enzymes,.. and scaffolding proteins..”
    http: //en.wikipedia.org/wiki/Poly_ADP_ribose_polymerase

    Mapping the role of NAD metabolism in prevention and treatment of carcinogenesis.

    “We show that nicotinamide and the resulting cellular NAD concentration modulate expression of the tumor suppressor protein, p53, in human breast, skin, and lung cells. Studies to determine the optimal NAD concentrations for responding to DNA damage in breast epithelial cells reveal that DNA damage appears to stimulate NAD biosynthesis and that recovery from DNA damage occurs several hours earlier in the presence of higher NAD or in cells undergoing active NAD biosynthesis.”

    http://www.ncbi.nlm.nih.gov/pubmed/10331640

    “Nicotinamide adenine dinucleotide, abbreviated NAD+, is a coenzyme found in all living cells.”

    “In organisms, NAD+ can be synthesized from simple building-blocks (de novo) from the amino acids tryptophan or aspartic acid. In an alternative fashion, more complex components of the coenzymes are taken up from food as the vitamin called niacin”
    http: //en.wikipedia.org/wiki/Nicotinamide_adenine_dinucleotide

    Ribose
    “Ribose was first reported in 1891 by Emil Fischer. It is a C’-2 carbon epimer of the sugar D-arabinose (both isomers of which are named for their source, gum arabic) and ribose itself is named as a transposition of the name of arabinose.

    Ribose constitutes the backbone of RNA, a biopolymer that is the basis of genetic transcription.”
    http: //en.wikipedia.org/wiki/Ribose

    “Ribose is produced naturally in our bodies. It is synthesized from glucose and is a valuable source of energy”

    Would that be the much vilified sugar?

    To my untutored mind that looks very much like some kind of combined glue and alarm system for dealing with DNA strand breaks and if you run out of any of the components that make it, the pattern of the cells will not be able to replicate or delete themselves correctly and descend into chaos.

  5. harleyrider1978 says:

    Watch the IPA’s James Paterson debate Australia’s biggest Nanny Stater, Simon Chapman, on ludicrous calls to ban smoking.

  6. garyk30 says:

    Cancer cells, especially lung cancer ones, are very strange critters and need to be looked at from different views.

    Funny thing about the comparative risks for lung cancer death and the number of cigs smoked per day.

    Data from Doll’s ’50 year study of doctors’ mortality’.

    Now we travel with Alice thru the looking glass into the land of paradoxes.

    30 times as much smoked does not equal 30 times as much lung cancer.

    Never-smokers have 0.17 lung cancer deaths per 19.38 total deaths per year.
    That is about 1%(0.9%)

    Smokers of:
    1-14 cigs/day had 1.31 lung cancer deaths per 29.34 total deaths.
    That is 4.5%

    25+ cigs/day had 4.17 lung cancer deaths per 45.34 total deaths.
    That is 9.2%

    Funny Facts:
    A smoker of 1 cig/day had 4.5 times the rate of lung cancer death as a never-smoker.

    A smoker of 30 cigs/day would have only 9.2 times the lung cancer death rate of the never-smokers and only twice the rate of the 1 cig/day smokers.

    Yes, they would smoke 30 times as many cigs/day and only have twice the lung cancer death rate.

    Seems that I have read that to prove ‘causation’ you have to show a linear progression(straight line) between dose and effect.

    30 times as many cigs/day smoked must lead to 30 times as much lung cancer or else smoking cigs does not cause lung cancer.

    Somehow, Doll never gets around to mentioning this little fact!!!! :)

    Frank, perhaps your model can explain this obvious disparity in cause and effect?

  7. harleyrider1978 says:

    The commie believes in prohibition,imagine that!

  8. garyk30 says:

    Of course, Doll is an expert and I am only a cantankerous old smoker who is too fond of good red wine and champagne.

    I need a fancy, official sounding title/position.

    Perhaps we could start ‘The International Association of Tobacco Studies”?

    Frank could be the ‘Deputy Director For England’ and the ‘Assistant Director for Social Studies and Computor Models’.

    Rose could be the ‘Assistant Deputy Director for England’ and the ‘Assistant Director for Botanical and Chemical Studies’.

    I could be the ‘Assistant Deputy Director for the USA’ and the ‘Assistant Director for Health Scare Studies’.

    Now, there are some very official sounding positions/titles!!!!

    • garyk30 says:

      That should be ‘The International Association for Tobacco Studies”?

      That way we could have:
      ‘The ISIS Report’
      by C.Frank Davis:‘Assistant Director for Social Studies and Computer Models’
      ‘The International Association for Tobacco Studies”

      What a way to lead a press release!!!!

  9. garyk30 says:

    The International Association for Tobacco Studies” is not such a far feteched idea.

    Much of the work that Rose has done is of valid scientific importance.

    Rose and Junican have released a great deal of very important information about ‘Home Grown Tobacco’ , growing and curing.

    Harley has put together a lot of good info debunking TC claims.

    Harley, you could be:
    ‘The Assistant Deputy Director for the USA-Kentucky’
    ‘The Assistant Director for Exposing TC Lies’
    The International Association for Tobacco Studies”

  10. harleyrider1978 says:

    The Assistant Director for Exposing TC Lies’
    It takes all of us to debunk TC lies…….I just gather a massive library with nearly total recall for each and every TC claim. But always come back to the folks who know……..all of us!

    BTW your work is very important……….

    • garyk30 says:

      “BTW your work is very important……….”

      Dear ‘Assistant Director’ Harley,
      All of our work is important ; but, we need a wider audience than just ‘preaching’ to the choir!!!!

      A ‘International Association’ might be one way of getting acceptance into the media and publications.

      • harleyrider1978 says:

        YES I would agree totally………in many aspects we already have a vaster audience as the smoking and obesity trash criss cross the same subject utilizing the same junk science and tactics. While we maynot be actually openly getting in their sites in online debates TC inflicts more allies for us as their ever bigger nanny state encompasses more and more victims. This is theyre achilles hill………… As Hitler learned way to late, to many fronts in a war causes defeat! Because you got more folks after dat ass……….

  11. harleyrider1978 says:

    Actually its a slow day in TC propaganda today………..Cant find much out there.

  12. garyk30 says:

    Leg Iron has a PHD and has published numerous peer reviewed studies and he could be:

    Dr. Leg Iron PHD
    Executive Director and Chairman of the Board
    The International Association for Tobacco Studies

    The Board of Directors of The International Association for Tobacco Studies for starters could include:
    Dr. Leg Iron PHD
    Executive Director and Chairman of the Board

    Wiel Maesson
    Successful business man and political leader

    Chris Snowden
    Well known author and media presenter

    Mike MacFadden
    Author and Researcher

    Rose
    Well known amateur Botanist and researcher

  13. harleyrider1978 says:

    Hell all I wanna do and be is me sitting in my old waffle house with my life long friends like we use to do before the ban down in nashville. Since then Ive been at war and a long one at that! Never give up never give in. But in the end being left alone to smoke in our old hangouts amongst friends is all we really wanted. I cant think of any reason to stop fighting until that objective is met.

No need to log in

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s